Hi ,
I’m trying to import data by QIIME2 but I have issue with this.
This is example of my filenames format
W28_J0545_S100_L001_R1_001.fastq.gz W28_J0545_S170_L001_R1_001.fastq.gz W28_J0545_S31_L001_R1_001.fastq.gz
W28_J0545_S100_L001_R2_001.fastq.gz W28_J0545_S170_L001_R2_001.fastq.gz W28_J0545_S31_L001_R2_001.fastq.gz
W28_J0545_S101_L001_R1_001.fastq.gz W28_J0545_S171_L001_R1_001.fastq.gz W28_J0545_S32_L001_R1_001.fastq.gz
W28_J0545_S101_L001_R2_001.fastq.gz W28_J0545_S171_L001_R2_001.fastq.gz W28_J0545_S32_L001_R2_001.fastq.gz
W28_J0545_S102_L001_R1_001.fastq.gz W28_J0545_S172_L001_R1_001.fastq.gz W28_J0545_S33_L001_R1_001.fastq.gz
W28_J0545_S102_L001_R2_001.fastq.gz W28_J0545_S172_L001_R2_001.fastq.gz W28_J0545_S33_L001_R2_001.fastq.gz
W28_J0545_S103_L001_R1_001.fastq.gz W28_J0545_S173_L001_R1_001.fastq.gz W28_J0545_S34_L001_R1_001.fastq.gz
W28_J0545_S103_L001_R2_001.fastq.gz W28_J0545_S173_L001_R2_001.fastq.gz W28_J0545_S34_L001_R2_001.fastq.gz
W28_J0545_S104_L001_R1_001.fastq.gz W28_J0545_S174_L001_R1_001.fastq.gz W28_J0545_S35_L001_R1_001.fastq.gz
After I run this command,
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path m_28w \
--source-format CasavaOneEightSingleLanePerSampleDirFmt \
--output-path demux-paired-end.qza
I got this error:
There was a problem importing m_28w:
m_28w is not a(n) CasavaOneEightSingleLanePerSampleDirFmt:
Duplicate samples in forward reads: {'W28_J0545'}
I tried to remove W28 but still I have same issue.
Is there a way to solve this issue?
Thanks,
Sounds like the issue was just from some empty cells in your original manifest file. You should carry on with your analyses using the Phred33 format, the error you get with Phred64 is indicative of your data not being Phred64. Most modern Illumina machines do give you Phred33 format FASTQ files these days but if you really want to be sure you can ask your sequencing facility. Wikipedia has a nice